HDF5 Dataset Interface
These functions create and manipulate dataset objects, and set and retrieve their constant or persistent properties.
H5Dcreate (h5loc, name, dtype_id, h5space, lcpl=NULL, dcpl=NULL, dapl=NULL)
H5Dopen (h5loc, name, dapl=NULL)
H5Dclose (h5dataset)
H5Dget_space (h5dataset)
H5Dget_type (h5dataset)
H5Dget_create_plist (h5dataset)
H5Dget_storage_size (h5dataset)
H5Dread (h5dataset, h5spaceFile = NULL, h5spaceMem = NULL,
buf = NULL, compoundAsDataFrame = TRUE,
bit64conversion, drop = FALSE)
H5Dwrite (h5dataset, buf, h5spaceMem = NULL, h5spaceFile = NULL)
H5Dset_extent (h5dataset, size)h5loc |
An object of class |
name |
Name of the dataset (character). |
dtype_id |
A character name of a datatype. See |
h5space |
An object of class |
h5dataset |
An object of class |
h5spaceFile,h5spaceMem |
An object of class |
buf |
Reading and writing buffer containing the data to written/read. When using the buffer for reading, the buffer size has to fit the size of the memory space |
compoundAsDataFrame |
If true, a compound datatype will be coerced to a data.frame. This is not possible, if the dataset is multi-dimensional. Otherwise the compound datatype will be returned as a list. Nested compound data types will be returned as a nested list. |
bit64conversion |
Defines, how 64-bit integers are converted. Internally, R does not support 64-bit integers. All integers in R are 32-bit integers. By setting bit64conversion='int', a coercing to 32-bit integers is enforced, with the risc of data loss, but with the insurance that numbers are represented as integers. bit64conversion='double' coerces the 64-bit integers to floating point numbers. doubles can represent integers with up to 54-bits, but they are not represented as integer values anymore. For larger numbers there is again a data loss. bit64conversion='bit64' is recommended way of coercing. It represents the 64-bit integers as objects of class 'integer64' as defined in the package 'bit64'. Make sure that you have installed 'bit64'. The datatype 'integer64' is not part of base R, but defined in an external package. This can produce unexpected behaviour when working with the data. |
drop |
(logical) If TRUE, the HDF5 object is read as a vector with NULL dim attributes. |
size |
An integer vector with the new dimension of the dataset. Calling this function is only valid for chunked datasets. |
lcpl |
An object of class |
dcpl |
An object of class |
dapl |
An object of class |
Interface to the HDF5 C-library libhdf5. See https://portal.hdfgroup.org/display/HDF5/Datasets for further details.
H5Dcreate and H5Dopen return an object of class H5IdComponent represinting a H5 dataset identifier.
H5Dget_space returns an object of class H5IdComponent representing a H5 dataspace identifier.
H5Dread returns an array with the read data.
The other functions return the standard return value from their respective C-functions.
Bernd Fischer
# write a dataset
fid <- H5Fcreate("ex_H5D.h5")
fid
sid <- H5Screate_simple(c(10,5,3))
sid
did <- H5Dcreate(fid, "A", "H5T_STD_I32LE", sid)
did
H5Dwrite(did, 1L:150L, h5spaceMem = sid, h5spaceFile = sid)
H5Dclose(did)
H5Sclose(sid)
H5Fclose(fid)
# read a dataset
fid <- H5Fopen("ex_H5D.h5")
fid
did <- H5Dopen(fid, "A")
did
sid <- H5Dget_space(did)
sid
B <- H5Dread(did)
B
H5Dclose(did)
H5Sclose(sid)
H5Fclose(fid)
# write a subarray
fid <- H5Fopen("ex_H5D.h5")
fid
did <- H5Dopen(fid, "A")
did
sid <- H5Dget_space(did)
sid
H5Sselect_index(sid, list(1:3,2:4,2))
sidmem <- H5Screate_simple(c(3,3,1))
sidmem
A = array(-801:-809,dim=c(3,3,1))
H5Dwrite(did, A, h5spaceMem = sidmem, h5spaceFile = sid)
H5Dread(did)
H5Sclose(sid)
H5Dclose(did)
H5Sclose(sidmem)
H5Fclose(fid)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.